tebriz
Warlord
I think you put the civs in like this
BeginPlayer
Team=0
LeaderType=NONE
CivType=NONE
Color=NONE
ArtStyle=NONE
Handicap=HANDICAP_NOBLE
EndPlayer
BeginPlayer
Team=1
LeaderType=NONE
CivType=NONE
Color=NONE
ArtStyle=NONE
Handicap=HANDICAP_NOBLE
EndPlayer
this will make them random
This is how I have the lines:
BeginPlayer
Team=0
LeaderType=LEADER_GILGAMESH
LeaderName=TXT_KEY_LEADER_GILGAMESH
CivDesc=Sumerian Tribe
CivShortDesc=Sumeria
CivAdjective=Sumerian
FlagDecal=Art/Interface/TeamColor/FlagDECAL_Sumeria.dds
WhiteFlag=1
CivType=CIVILIZATION_SUMERIA
Color=PLAYERCOLOR_DARK_INDIGO
ArtStyle=ARTSTYLE_CRESCENT
PlayableCiv=1
MinorNationStatus=0
StartingGold=0
StartingX=48, StartingY=52
EndPlayer
BeginPlayer
Team=1
LeaderType=NONE
CivType=NONE
EndPlayer
BeginPlayer
Team=2
LeaderType=NONE
CivType=NONE
EndPlayer
I think it is same as you noticed...
As I said I try to make a map with one preset civilization Sumer, rest of civilizations to be random. But when I open custom scenario in order to add AI civilizations it doesn't allow me to add them

P.S. I even added the extra lines you mentioned:
Color=NONE
ArtStyle=NONE
Handicap=HANDICAP_NOBLE
It is same result, no difference